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fix: change source #192

Merged
merged 1 commit into from
Jan 23, 2025
Merged

fix: change source #192

merged 1 commit into from
Jan 23, 2025

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vedhav
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@vedhav vedhav commented Jan 23, 2025

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@vedhav vedhav enabled auto-merge (squash) January 23, 2025 14:44
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I'm surprised by this change. In the past I found several issues with renv and using Bioconductor.

When adding the Bioconductor repositories using the standard BiocManager I see these names for the repositories:

> repos <- BiocManager::repositories()
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cloud.r-project.org
> names(repos)
[1] "BioCsoft"      "BioCann"       "BioCexp"       "BioCworkflows" "BioCbooks"     "P3M"           "CRAN"  

The last 2 are the ones I have by default. But the Repository name is different.
Where does the "Bioconductor 3.19" comes from? Maybe this was created with a different renv version used to other PR

@vedhav vedhav merged commit 903482a into main Jan 23, 2025
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@vedhav vedhav deleted the fix@main branch January 23, 2025 15:03
@github-actions github-actions bot locked and limited conversation to collaborators Jan 23, 2025
@vedhav
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vedhav commented Jan 23, 2025

@llrs-roche I think it's a new way to specify BioC version in renv. Previously we used to also have the BioC repo links snapshotted at the top of the renv.lock file but now with this new syntax it can automatically detect and install it.

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3 participants